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| 1 | +#!/usr/bin/env Rscript |
| 2 | + |
| 3 | +# Script to update CRAN-like repository with a package release which points |
| 4 | +# to GitHub release assets. This allows us to maintain a CRAN-like website |
| 5 | +# for users to easily install packages while hosting the actual binaries |
| 6 | +# on GitHub releases. The script merges new package entries with existing |
| 7 | +# ones in the PACKAGES file or creates it if it doesn't exist. |
| 8 | +# |
| 9 | +# CRAN like directory structure using the posit style structure for linux, treat |
| 10 | +# it as if it were a source distribution and not binary |
| 11 | +# (https://docs.posit.co/rspm/admin/serving-binaries.html). |
| 12 | +# CRAN does not distribute linux binaries, so nothing to mimic there. |
| 13 | +# Each version gets its own directory under the base CRAN directory, |
| 14 | +# |
| 15 | +# vMAJOR.MINOR.PATCH/ |
| 16 | +# │ |
| 17 | +# ├── __linux__/ (using posit structure for source packages) |
| 18 | +# │ ├── ubuntu-noble/ |
| 19 | +# │ │ ├── 4.4 |
| 20 | +# │ │ └── src/ |
| 21 | +# │ │ └── contrib/ |
| 22 | +# │ │ ├── PACKAGES |
| 23 | +# │ │ ├── PACKAGES.gz |
| 24 | +# │ │ ├── PACKAGES.rds |
| 25 | +# │ │ └── package_version.tar.gz (omitted in our case) |
| 26 | +# │ ├── rhel9/ |
| 27 | +# │ ├── 4.4 |
| 28 | +# │ └── src/ |
| 29 | +# │ └── contrib/ |
| 30 | +# │ ├── PACKAGES |
| 31 | +# │ ├── PACKAGES.gz |
| 32 | +# │ ├── PACKAGES.rds |
| 33 | +# │ └── package_version.tar.gz (omitted in our case) |
| 34 | +# │ |
| 35 | +# ├── bin/ |
| 36 | +# ├── windows/ |
| 37 | +# │ └── contrib/ |
| 38 | +# │ └── 4.4/ |
| 39 | +# │ ├── PACKAGES |
| 40 | +# │ ├── PACKAGES.gz |
| 41 | +# │ ├── PACKAGES.rds |
| 42 | +# │ └── package_version.zip (omitted in our case) |
| 43 | +# └── macosx/ |
| 44 | +# ├── contrib/ (intel) |
| 45 | +# │ └── 4.4/ |
| 46 | +# │ ├── PACKAGES |
| 47 | +# │ ├── PACKAGES.gz |
| 48 | +# │ ├── PACKAGES.rds |
| 49 | +# │ └── package_version.tgz (omitted in our case) |
| 50 | +# ├── big-sur-arm64/ |
| 51 | +# │ └── contrib/ |
| 52 | +# │ └── 4.4/ |
| 53 | +# │ ├── PACKAGES |
| 54 | +# │ ├── PACKAGES.gz |
| 55 | +# │ ├── PACKAGES.rds |
| 56 | +# │ └── package_version.tgz (omitted in our case) |
| 57 | +# └── sonoma-arm64/ |
| 58 | +# └── contrib/ |
| 59 | +# └── 4.6/ |
| 60 | +# ├── PACKAGES |
| 61 | +# ├── PACKAGES.gz |
| 62 | +# ├── PACKAGES.rds |
| 63 | +# └── package_version.tgz (omitted in our case) |
| 64 | +# |
| 65 | +# |
| 66 | +# Usage: |
| 67 | +# Rscript update_cran_repo.R --packages_dir <path> --base_cran_dir <path> --repo_url <url> --tag <tag> |
| 68 | +# |
| 69 | +# Arguments: |
| 70 | +# --packages_dir Directory containing downloaded package files. The package |
| 71 | +# files are expected to be named in the format: |
| 72 | +# SimpleITK_{VERSION}_R{R_VERSION}_{PLATFORM}.{extension} |
| 73 | +# --base_cran_dir Base directory for CRAN-like repository (e.g., "docs" for a GitHub pages site) |
| 74 | +# --repo_url URL of the GitHub repository storing the binary files as release assets (e.g., https://github.com/user/repo) |
| 75 | +# --tag Release tag name (e.g. v2.5.5) |
| 76 | +# |
| 77 | +# Example: |
| 78 | +# Rscript update_cran_repo.R \ |
| 79 | +# --packages_dir temp_packages \ |
| 80 | +# --base_cran_dir docs \ |
| 81 | +# --repo_url https://github.com/SimpleITK/SimpleITKRInstaller \ |
| 82 | +# --tag v2.5.5 |
| 83 | + |
| 84 | +library(tools) |
| 85 | + |
| 86 | +# Utility function to merge and sort package entries |
| 87 | +merge_packages <- function(existing_packages, new_package, new_url, version) { |
| 88 | + # Replace or add "File" field from write_PACKAGES with release URL, |
| 89 | + # ensures PACKAGES has a single File entry. |
| 90 | + if (!is.null(colnames(new_package)) && "File" %in% colnames(new_package)) { |
| 91 | + new_package <- new_package[, colnames(new_package) != "File", drop = FALSE] |
| 92 | + } |
| 93 | + new_package <- cbind(new_package, File = new_url) |
| 94 | + |
| 95 | + # Combine with existing packages |
| 96 | + if (!is.null(existing_packages) && nrow(existing_packages) > 0) { |
| 97 | + # Remove any existing entry for the same version (to handle re-releases) |
| 98 | + existing_packages <- existing_packages[existing_packages[, "Version"] != version, , drop = FALSE] |
| 99 | + all_packages <- rbind(new_package, existing_packages) |
| 100 | + } else { |
| 101 | + all_packages <- new_package |
| 102 | + } |
| 103 | + |
| 104 | + # Sort by version (newest first) |
| 105 | + if (nrow(all_packages) > 1) { |
| 106 | + versions <- package_version(all_packages[, "Version"]) |
| 107 | + all_packages <- all_packages[order(versions, decreasing = TRUE), , drop = FALSE] |
| 108 | + } |
| 109 | + |
| 110 | + return(all_packages) |
| 111 | +} |
| 112 | + |
| 113 | +# Parse command-line arguments in --key value format |
| 114 | +# Takes a character vector of arguments and returns a named list |
| 115 | +# Validates that all required arguments are present and that no consecutive keys are present |
| 116 | +# Example: c("--packages_dir", "temp", "--tag", "v1.0") -> list("packages_dir" = "temp", "tag" = "v1.0") |
| 117 | +parse_args <- function(args, required_args = NULL) { |
| 118 | + parsed <- list() |
| 119 | + i <- 1 |
| 120 | + while (i <= length(args)) { |
| 121 | + if (startsWith(args[i], "--")) { |
| 122 | + key <- sub("^--", "", args[i]) |
| 123 | + if (i < length(args) && !startsWith(args[i + 1], "--")) { |
| 124 | + parsed[[key]] <- args[i + 1] |
| 125 | + i <- i + 2 |
| 126 | + } else { |
| 127 | + stop(sprintf("Missing or invalid value for argument: --%s", key)) |
| 128 | + } |
| 129 | + } else { |
| 130 | + stop(sprintf("Unexpected argument format: %s (expected a key starting with --)", args[i])) |
| 131 | + } |
| 132 | + } |
| 133 | + # Validate required arguments |
| 134 | + if (!is.null(required_args)) { |
| 135 | + missing_args <- setdiff(required_args, names(parsed)) |
| 136 | + if (length(missing_args) > 0) { |
| 137 | + stop("Missing required arguments: ", paste(missing_args, collapse = ", ")) |
| 138 | + } |
| 139 | + } |
| 140 | + return(parsed) |
| 141 | +} |
| 142 | + |
| 143 | + |
| 144 | + |
| 145 | +# Package platform to [repository path, type] mapping |
| 146 | +platform_map <- list( |
| 147 | + "windows-x86_64" = list(path = "bin/windows/contrib", type = "win.binary"), |
| 148 | + "macos-x86_64" = list(path = "bin/macosx/contrib", type = "mac.binary"), |
| 149 | + "macos-arm64" = list(path = "bin/macosx/big-sur-arm64/contrib", type = "mac.binary"), |
| 150 | + "linux-x86_64" = list(path = "__linux__/ubuntu-noble", type = "source") |
| 151 | +) |
| 152 | + |
| 153 | +# Expected package filename pattern |
| 154 | +package_pattern <- "^SimpleITK_([^_]+)_R([0-9]+\\.[0-9]+)_([^\\.]+)\\.(.*)$" |
| 155 | + |
| 156 | +# Parse command line arguments |
| 157 | +args <- commandArgs(trailingOnly = TRUE) |
| 158 | +parsed_args <- parse_args(args, required_args = c("packages_dir", "base_cran_dir", "repo_url", "tag")) |
| 159 | + |
| 160 | +packages_dir <- parsed_args[["packages_dir"]] |
| 161 | +base_cran_dir <- parsed_args[["base_cran_dir"]] |
| 162 | +repo_url <- parsed_args[["repo_url"]] |
| 163 | +tag <- parsed_args[["tag"]] |
| 164 | +effective_base_cran_dir <- file.path(base_cran_dir, tag) |
| 165 | + |
| 166 | +# Validate packages directory exists |
| 167 | +if (!dir.exists(packages_dir)) { |
| 168 | + quit(save = "no", status = 0) |
| 169 | +} |
| 170 | + |
| 171 | +# Get all files in packages_dir that match the expected pattern |
| 172 | +all_files <- list.files(packages_dir, full.names = TRUE) |
| 173 | +files <- all_files[grepl(package_pattern, basename(all_files))] |
| 174 | + |
| 175 | +for (file in files) { |
| 176 | + tryCatch({ |
| 177 | + filename <- basename(file) |
| 178 | + |
| 179 | + matches <- regmatches(filename, regexec(package_pattern, filename))[[1]] |
| 180 | + version <- matches[2] |
| 181 | + r_version <- matches[3] |
| 182 | + platform <- matches[4] |
| 183 | + extension <- matches[5] |
| 184 | + |
| 185 | + if (!platform %in% names(platform_map)) { |
| 186 | + message("Unknown platform: ", platform) |
| 187 | + next |
| 188 | + } |
| 189 | + |
| 190 | + # Create destination directory |
| 191 | + platform_info <- platform_map[[platform]] |
| 192 | + dest_dir <- if (platform_info$type == "source") { |
| 193 | + file.path(effective_base_cran_dir, platform_info$path, r_version, "src", "contrib") |
| 194 | + } else { |
| 195 | + file.path(effective_base_cran_dir, platform_info$path, r_version) |
| 196 | + } |
| 197 | + dir.create(dest_dir, recursive = TRUE, showWarnings = FALSE) |
| 198 | + |
| 199 | + # Read existing PACKAGES file BEFORE it gets overwritten |
| 200 | + packages_file <- file.path(dest_dir, "PACKAGES") |
| 201 | + existing_packages <- if (file.exists(packages_file)) { |
| 202 | + read.dcf(packages_file) |
| 203 | + } else { |
| 204 | + NULL |
| 205 | + } |
| 206 | + |
| 207 | + # Copy file temporarily to generate PACKAGES metadata |
| 208 | + cleaned_name <- sprintf("SimpleITK_%s.%s", version, extension) |
| 209 | + temp_dest <- file.path(dest_dir, cleaned_name) |
| 210 | + if (!file.copy(file, temp_dest, overwrite = TRUE)) { |
| 211 | + stop(sprintf("Failed to copy %s to %s", file, temp_dest)) |
| 212 | + } |
| 213 | + |
| 214 | + # Generate PACKAGES file with metadata from the binary (this overwrites existing) |
| 215 | + write_PACKAGES(dest_dir, type = platform_map[[platform]]$type, latestOnly = FALSE) |
| 216 | + |
| 217 | + # Read the newly generated package entry |
| 218 | + new_package <- read.dcf(packages_file) |
| 219 | + |
| 220 | + # Merge with existing packages and sort, also adds |
| 221 | + # the File field using GitHub URL |
| 222 | + merged_packages <- merge_packages(existing_packages, |
| 223 | + new_package, |
| 224 | + sprintf("%s/releases/download/%s/%s", repo_url, tag, filename), |
| 225 | + version) |
| 226 | + |
| 227 | + # Write merged PACKAGES file |
| 228 | + write.dcf(merged_packages, packages_file) |
| 229 | + |
| 230 | + # Generate compressed version |
| 231 | + gzf <- gzfile(file.path(dest_dir, "PACKAGES.gz"), "w") |
| 232 | + write.dcf(merged_packages, gzf) |
| 233 | + close(gzf) |
| 234 | + |
| 235 | + # Generate PACKAGES.rds version |
| 236 | + saveRDS(merged_packages, file.path(dest_dir, "PACKAGES.rds"), version = 2) |
| 237 | + |
| 238 | + # Remove the temporary binary package file from the CRAN-like directory |
| 239 | + unlink(temp_dest) |
| 240 | + }, error = function(e) { |
| 241 | + message(sprintf("Error processing file %s: %s", file, e$message)) |
| 242 | + quit(save = "no", status = 1) |
| 243 | + }) |
| 244 | +} |
| 245 | + |
| 246 | + |
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